For first time in 60 years, spring-run Chinook salmon reproduce in San Joaquin River

As work to restore the San Joaquin River continues, scientists are seeing promising signs that salmon can thrive in the river as hatchery fish reach new milestones.

A recent breakthrough came in fall 2017, when spring-run Chinook salmon created their nests, called redds, in the colder parts of the river below Friant Dam. The fish successfully spawned, laying eggs that incubated and hatched into tiny fry as the sexually mature fish died, part of the species’ unusual life cycle.

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“Having these spring-run spawn in the river really starts to build scientific evidence that yes, spawning is possible,” said Alicia Forsythe, the restoration program manager. “One year doesn’t prove that this is going to work in the future and everything is great…We definitely need to see a number of years of data to help us come to those conclusions. But, it’s promising.”

Spring-run Chinook essentially disappeared from the San Joaquin after the Friant Dam was completed in the 1940s, drying out a 60-mile stretch of the river for more than half a century. Salmon couldn’t complete their journey back from the ocean to the river where they reproduce.

Federal officials, farmers and conservationists in 2006 ended an 18-year lawsuit with a settlement to reconnect the river with the ocean and revive long-dead salmon runs. Experimental flows began in 2009. The settlement’s two goals are to restore the river and fish populations while continuing to honor water rights and provide irrigation supplies to farmers.

The wet winter in 2016-2017 provided better springtime conditions for the spring-run Chinook, making it possible for them to “hold,” or hang out, in those deep river pockets near the dam over the summer and spawn in August and September, according to Don Portz, the lead biologist for the restoration program. The flood event kept river temperatures cool and made it harder for predatory fish species, such as the black bass, to prey on juvenile salmon.

Even without a wet winter, river conditions should provide suitable spawning habitat for the fish, Forsythe said. Additional water, called restoration flows, began Jan. 1, 2014, but they were discontinued in 2014 and 2015 due to the punishing drought that ravaged the San Joaquin Valley and Sierra Nevada. The river reconnected from Friant to the Merced River in August 2016.

Since the settlement, biologists began taking juveniles and then eggs from spring-run Chinook in northern areas of the state and rearing fry in a hatchery before releasing them in the San Joaquin to monitor them.

In January, about 80,000 fish were released into the river. About 100,000 additional spring-run juveniles will be released in March. Some of those juveniles have been tagged with acoustic transmitters for tracking.

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The new facility, which is expected to produce 1 million fish to be released into the river per year, is expected to be completed in September. Craig KohlrussThe Fresno Bee

In February, biologists will keep an eye out for spring-run Chinook returning from the ocean and Sacramento-San Joaquin Delta to the downstream part of the river, where the San Joaquin and Merced rivers meet.

Kole Upton, a Chowchilla farmer who helped negotiate the settlement a dozen years ago, worries in the future the salmon won’t be able to make the journey from the sea to Friant, especially in years like this where rain is scarce and the Sierra snowpack is tenuous. He also believes that with climate change, the San Joaquin River temperatures won’t remain cool enough for salmon species.

“In theory, if they can spawn, yeah, I agree that shows it’s feasible,” he said. “But the San Joaquin River is a flat river. It’s not a deep gorge river like the Tuolumne. In that kind of environment, the salmon have a harder time surviving because they’re temperature dependent.”

To satisfy both goals of the settlement – restoring the river and fish populations and delivering water to farmers – Upton said a warm-water fishery might be more realistic.

“It’s fine to have goals,” he said. “But I think you have to be realistic and look at the effects on other members of society. I’m afraid it’s not going to be feasible (restoring salmon) because of climate warming.”

The restoration program is looking forward to construction projects in the near future that will remove barriers in the river blocking the salmon from freely traveling up and down the San Joaquin.

One of those is the Mendota Pool Bypass project, which will provide fish passage around Mendota Pool by creating a new channel free of barriers such as fish screens and a gate. Mendota Pool is a central hub for irrigation water diversions where water comes in and goes out through the Delta-Mendota canal. This project will expand 11 miles of river and triple the channel’s capacity, Forsythe said.

Construction is set to begin in fall 2019 and will last about six years, said Josh Newcom, public affairs specialist for the restoration program. The project has been a long time coming after being pushed back multiple times while the restoration program worked to secure seepage easements.

The program also already started construction in March 2017 on a new hatchery near the Friant Dam. The new facility will house a million juvenile fish, about four times more than the current facility’s capacity. That will allow for maximum genetic diversity, said Brian Erlandsen, a senior environmental scientist with the California Department of Fish and Wildlife, which works with the restoration program. Construction on the new hatchery is due to be complete this fall.